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Selection: with tag free-scientific-software [92 articles] 

 

Steps towards transparency in research publishing

  
Nature, Vol. 549, No. 7673. (26 September 2017), pp. 431-431, https://doi.org/10.1038/549431a

Abstract

As research and editorial processes become increasingly open, scientists and editors need to be proactive but also alert to risks. [Excerpt] [...] The examples given here relate to initiatives by the Nature Research journals, some of which follow pioneering work by other publishers. [...] One such initiative is the checklist introduced by Nature and the Nature journals in 2013 for life-sciences submissions. [...] Malcolm Macleod of the University of Edinburgh, UK, and his colleagues [..] looked at the completeness of reporting in journals ...

 

Robust modelling of the impacts of climate change on the habitat suitability of forest tree species

  
Keywords: abies-alba   array-of-factors   artificial-neural-networks   bioclimatic-predictors   change-factor   climate-change   data-uncertainty   diversity   environmental-modelling   europe   extrapolation-uncertainty   featured-publication   forest-resources   free-scientific-knowledge   free-scientific-software   free-software   fuzzy   gdal   genetic-diversity   geospatial   geospatial-semantic-array-programming   gnu-bash   gnu-linux   gnu-octave   habitat-suitability   integration-techniques   mastrave-modelling-library   maximum-habitat-suitability   modelling-uncertainty   multiplicity   peseta-series   python   regional-climate-models   relative-distance-similarity   robust-modelling   semantic-array-programming   semantic-constraints   semantics   spatial-disaggregation   sres-a1b   supervised-training   unsupervised-training  

Abstract

[::] In Europe, forests play a strategic multifunctional role, serving economic, social and environmental purposes. However, their complex interaction with climate change is not yet well understood. [::] The JRC PESETA project series proposes a consistent multi-sectoral assessment of the impacts of climate change in Europe. [::] Within the PESETA II project, a robust methodology is introduced for modelling the habitat suitability of forest tree species (2071-2100 time horizon). [::] Abies alba (the silver fir) is selected as case study: a main European tree ...

References

  1. European Commission, 2013. Communication from the Commission to the European Parliament, the Council, the European Economic and Social Committee and the Committee of the Regions - A new EU forest strategy: for forests and the forest based sector. No. COM(2013) 659 final. Communication from the Commission to the Council and the European Parliament. http://eur-lex.europa.eu/legal-content/EN/TXT/?uri=celex:52013DC0659 , INRMM-MiD:12642065 .
  2. European Commission, 2013. Commission staff working document accompanying the document: Communication from the commission to
 

Bash reference manual: reference documentation for Bash edition 4.4, for Bash version 4.4

  
(2016)

Abstract

[Excerpt: Introduction] [::What is Bash?] Bash is the shell, or command language interpreter, for the GNU operating system. The name is an acronym for the ‘Bourne-Again SHell’, a pun on Stephen Bourne, the author of the direct ancestor of the current Unix shell sh, which appeared in the Seventh Edition Bell Labs Research version of Unix. [\n] Bash is largely compatible with sh and incorporates useful features from the Korn shell ksh and the C shell csh. It is intended to be a ...

 

Multi-dimensional weighted median: the module "wmedian" of the Mastrave modelling library

  
In Semantic Array Programming with Mastrave - Introduction to Semantic Computational Modelling (2012)

Abstract

Weighted median (WM) filtering is a well known technique for dealing with noisy images and a variety of WM-based algorithms have been proposed as effective ways for reducing uncertainties or reconstructing degraded signals by means of available information with heterogeneous reliability. Here a generalized module for applying weighted median filtering to multi-dimensional arrays of information with associated multi-dimensional arrays of corresponding weights is presented. Weights may be associated to single elements or to groups of elements along given dimensions of the ...

 

When free software isn't (practically) superior

  
GNU Operating System (2011)

Abstract

[Excerpt] The Open Source Initiative's mission statement reads, “Open source is a development method for software that harnesses the power of distributed peer review and transparency of process. The promise of open source is better quality, higher reliability, more flexibility, lower cost, and an end to predatory vendor lock-in.” [\n] For more than a decade now, the Free Software Foundation has argued against this “open source” characterization of the free software movement. Free software advocates have primarily argued against this framing because ...

 

Research software sustainability: report on a knowledge exchange workshop

  
(February 2016)

Abstract

[Excerpt: Executive summary] Without software, modern research would not be possible. Understandably, people tend to marvel at results rather than the tools used in their discovery, which means the fundamental role of software in research has been largely overlooked. But whether it is widely recognised or not, research is inexorably connected to the software that is used to generate results, and if we continue to overlook software we put at risk the reliability and reproducibility of the research itself. [\n] The adoption of software is accompanied by new risks - many of ...

 

Software and scholarship

  
Interdisciplinary Science Reviews, Vol. 40, No. 4. (2 October 2015), pp. 342-348, https://doi.org/10.1080/03080188.2016.1165456

Abstract

[excerpt] The thematic focus of this issue is to examine what happens where software and scholarship meet, with particular reference to digital work in the humanities. Despite the some seven decades of its existence, Digital Humanities continues to struggle with the implications, in the academic ecosystem, of its position between engineering and art. [...] [\n] [...] [\n] I will end with my own reflection on this topic of evaluation. Peer review of scholarly works of software continues to pose a particularly vexed challenge ...

 

Software search is not a science, even among scientists

  
(8 May 2016)

Abstract

When they seek software for a task, how do people go about finding it? Past research found that searching the Web, asking colleagues, and reading papers have been the predominant approaches---but is it still true today, given the popularity of Facebook, Stack Overflow, GitHub, and similar sites? In addition, when users do look for software, what criteria do they use? And finally, if resources such as improved software catalogs were to be developed, what kind of information would people want in them? These questions motivated our cross-sectional survey ...

 

optiminterp

  
In Free Software Directory (July 2009)

Abstract

An optimal interpolation toolbox for Octave. This package provides functions to perform a n-dimensional optimal interpolations of arbitrarily distributed data points ...

 

Promoting research resource identification at JCN

  
Journal of Comparative Neurology, Vol. 522, No. 8. (01 June 2014), pp. 1707-1707, https://doi.org/10.1002/cne.23585

Abstract

[Excerpt] [\n] [...] [\n] The attention of scientists, editors, and policymakers alike have all turned recently to the issue of reproducibility in scientific research, focusing on research spanning from the pharmaceutical industry (Begley and Ellis, 2012) to the highest levels of government (Collins and Tabak, 2014; see also McNutt, 2014). While these commentaries point out that scientific misconduct is quite rare, they do point to a confluence of factors that hinder the reproducibility of scientific findings, including the identification of key reagents, such ...

 

EucaTool®, a cloud computing application for estimating the growth and production of Eucalyptus globulus Labill. plantations in Galicia (NW Spain)

  
Forest Systems, Vol. 24, No. 3. (03 December 2015), eRC06, https://doi.org/10.5424/fs/2015243-07865

Abstract

[Aim of study] To present the software utilities and explain how to use EucaTool®, a free cloud computing application developed to estimate the growth and production of seedling and clonal blue gum (Eucalyptus globulus Labill.) plantations in Galicia (NW Spain). [Area of study] Galicia (NW Spain). [Material and methods] EucaTool® implements a dynamic growth and production model that is valid for clonal and non-clonal blue gum plantations in the region. The model integrates transition functions for dominant height (site index curves), number of ...

 

Updated source code for calculating fire danger indices in the Canadian Forest Fire Weather Index System

  
Vol. NOR-X-424 (2015)

Abstract

This report presents updated versions of the FORTRAN 77 program originally published by the Canadian Forest Service in 1985 and used to calculate the Canadian forest fire weather indices from daily weather observations. The updated program is presented here in FORTRAN 95, C, C++, Python, Java and SAS/IML programming languages to meet the needs of various users. The updated versions are easier to understand and use than the original source code. The updated source codes were written in a modular programming style, consisting of a main program and ...

References

  1. Canadian Forestry Service. 1984. Tables for the Canadian Forest Fire Weather Index System. (4th ed.) Environ. Can., Can. For. Serv., Ottawa, ON. For. Tech. Rep. 25. Also available at http://cfs.nrcan.gc.ca/pubwarehouse/pdfs/31168.pdf .
  2. Chapman, S. J. 2004. FORTRAN 90/95 for scientists and engineers. McGraw Hill Higher Education, Toronto, ON. Also available at http://www.mhhe.com/engcs/general/chapman/index.mhtml .
  3. De Groot, W.J.; Field, R.D.; Brady, M.A.; Roswintiarti, O.; Mohamad, M. 2006. Development of the
 

The Resource Identification Initiative: a cultural shift in publishing

  
Neuroinformatics, Vol. 14, No. 2. (2016), pp. 169-182, https://doi.org/10.1007/s12021-015-9284-3

Abstract

A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to identify the exact resources that are reported or to answer basic questions such as “How did other studies use resource X?” To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in ...

 

(INRMM-MiD internal record) List of keywords of the INRMM meta-information database - part 14

  
(February 2014)
Keywords: forest-fires   forest-floor-low-light-availability   forest-focus   forest-focus-monitoring   forest-inventories   forest-land-reclamation   forest-loss   forest-management   forest-pathogens   forest-pests   forest-product   forest-regeneration   forest-reproductive-material   forest-resource-information   forest-resources   forest-species   forest-species-composition   forest-structure   forest-succession   forest-types   forest-watering   forestcommunities   forestry   forestry-statistics   fortran   fossil-energy   fossil-resources   fp7-european-research-project   fracking   fractal   fragmentation   fragmented-world   frainetto   france   frangula-alnus   frangula-spp   fraxinus   fraxinus-angustifolia   fraxinus-augustifolia   fraxinus-excelsior   fraxinus-mandshurica   fraxinus-ornus   fraxinus-pennsylvanica   fraxinus-spp   free-access   free-access-book   free-riders   free-science-metrics   free-scientific-knowledge   free-scientific-software   free-software   free-software-directory   free-software-license-definition   freedom   freemat   french-alps   frequency   frost-resistance   frost-sensitivity   fruticosa   fuel   fuel-moisture   fuelwood   functional-connectivity   functional-descriptors   functional-programming   functional-traits   fungal-decay   fungal-diseases   fungi   fusarium-circinatum   fusarium-lateritium   future   future-climatic-envelopes   future-earth   future-internet   future-trends   fuzzy   gaia   galanthus-plicatus   galicia   gall-attributes   game-theory   gardening   gargano   garrulus-glandarius   gbif   gc-ms   gcm   gdal   gemmae-populi   gender-biases   gene-bank   gene-conservation   general-relation   generalized-additive-model   generalized-additive-models   generalized-linear-model   inrmm-list-of-tags  

Abstract

List of indexed keywords within the transdisciplinary set of domains which relate to the Integrated Natural Resources Modelling and Management (INRMM). In particular, the list of keywords maps the semantic tags in the INRMM Meta-information Database (INRMM-MiD). [\n] The INRMM-MiD records providing this list are accessible by the special tag: inrmm-list-of-tags ( http://mfkp.org/INRMM/tag/inrmm-list-of-tags ). ...

 

Adding terms to the GPL

  
MMM Tech Law & Business Report (2014), 7921

Abstract

[Excerpt] Many of us are called to review our clients’ use of open source software. Frequently, we are given a report with the name of the software and the name of the license to that software, with nothing else. One can then look up the open source license, often from a neutral source such as The Open Source Initiative’s website, where the text of many open source software licenses can be found. [\n] This process of reviewing open source licenses is only accurate if the license ...

 

The unsung heroes of scientific software

  
Nature, Vol. 529, No. 7584. (4 January 2016), pp. 115-116, https://doi.org/10.1038/529115a

Abstract

Creators of computer programs that underpin experiments don’t always get their due — so the website Depsy is trying to track the impact of research code. [Excerpt] For researchers who code, academic norms for tracking the value of their work seem grossly unfair. They can spend hours contributing to software that underpins research, but if that work does not result in the authorship of a research paper and accompanying citations, there is little way to measure its impact. [\n] [...] Depsy’s creators hope that their ...

 

GRASS GIS manual: r.li

  
In GRASS Development Team, 2014. GRASS GIS 7.1svn Reference Manual (2014)

Abstract

[Excerpt] The r.li suite is a toolset for multiscale analysis of landscape structure. It aims at implementing metrics as found in external software for quantitative measures of landscape structure like FRAGSTATS (McGarigal and Marks 1995). [\n] The r.li suite offers a set of patch and diversity indices. It supports analysis of landscapes composed of a mosaic of patches, but, more generally, the modules work with any two-dimensional raster map whose cell values are integer (e.g., 1, 2) or floating point (e.g., 1.1, ...

 

GRASS GIS manual: v.surf.rst

  
In GRASS Development Team, 2014. GRASS GIS 7.1svn Reference Manual (2014)

Abstract

v.surf.rst - Performs surface interpolation from vector points map by splines. Spatial approximation and topographic analysis from given point or isoline data in vector format to floating point raster format using regularized spline with tension. ...

 

pktools

  
(2015)

Abstract

[Introduction] pktools is a collection of programs written in C++ for image processing with a focus on remote sensing applications. It relies on the Geospatial Data Abstraction Library (GDAL, http://www.gdal.org) and OGR. [\n] All utilities in pktools use command line options and have a built in help [::] use the -h option to get help [::] pktools ALWAYS use -i for input and -o for output (unlike GDAL utilities that commonly use last argument as output and second but last argument as input) ...

 

Open code for open science?

  
Nature Geoscience, Vol. 7, No. 11. (30 October 2014), pp. 779-781, https://doi.org/10.1038/ngeo2283

Abstract

Open source software is often seen as a path to reproducibility in computational science. In practice there are many obstacles, even when the code is freely available, but open source policies should at least lead to better quality code. ...

 

GRASS GIS manual: r.watershed

  
In GRASS Development Team, 2014. GRASS GIS 7.1svn Reference Manual (2014)

Abstract

r.watershed - Calculates hydrological parameters and RUSLE factors. ...

 

GRASS GIS manual: r.slope.aspect

  
In GRASS Development Team, 2014. GRASS GIS 7.1svn Reference Manual (2004)

Abstract

r.slope.aspect - Generates raster maps of slope, aspect, curvatures and partial derivatives from an elevation raster map. Aspect is calculated counterclockwise from east. ...

References

  1. Horn, B. K. P. (1981). Hill Shading and the Reflectance Map, Proceedings of the IEEE, 69(1):14-47.
  2. Mitasova, H. (1985). Cartographic aspects of computer surface modeling. PhD thesis. Slovak Technical University , Bratislava
  3. Hofierka, J., Mitasova, H., Neteler, M., 2009. Geomorphometry in GRASS GIS. In: Hengl, T. and Reuter, H.I. (Eds), Geomorphometry: Concepts, Software, Applications. Developments in Soil Science, vol. 33, Elsevier, 387-410 pp, http://www.geomorphometry.org
 

Conefor Sensinode 2.2: A software package for quantifying the importance of habitat patches for landscape connectivity

  
Environmental Modelling & Software, Vol. 24, No. 1. (January 2009), pp. 135-139, https://doi.org/10.1016/j.envsoft.2008.05.005

Abstract

Maintaining and restoring landscape connectivity is currently a central concern in ecology and biodiversity conservation, and there is an increasing demand of user-driven tools for integrating connectivity in landscape planning. Here we describe the new Conefor Sensinode 2.2 (CS22) software, which quantifies the importance of habitat patches for maintaining or improving functional landscape connectivity and is conceived as a tool for decision-making support in landscape planning and habitat conservation. CS22 is based on graph structures, which have been suggested to possess ...

 

Knowledge Freedom in computational science: a two stage peer-review process with KF eligibility access review

  

Abstract

Wide scale transdisciplinary modelling (WSTM) growingly demands a focus on reproducible research and scientific knowledge freedom. Data and software freedom are essential aspects of knowledge freedom in computational science. Therefore, ideally published articles should also provide the readers with the data and source code of the described mathematical modelling. To maximise transparency, replicability, reproducibility and reusability, published data should be made available as open data while source code should be made available as free software. Here, a two-stage peer review process ...

Visual summary

 

Open Source Geospatial Tools - Applications in Earth Observation

  

Abstract

This book focuses on the use of open source software for geospatial analysis. It demonstrates the effectiveness of the command line interface for handling both vector, raster and 3D geospatial data. Appropriate open-source tools for data processing are clearly explained and discusses how they can be used to solve everyday tasks. A series of fully worked case studies are presented including vector spatial analysis, remote sensing data analysis, landcover classification and LiDAR processing. A hands-on introduction to the application programming interface (API) ...

 

Code share

  
Nature, Vol. 514, No. 7524. (29 October 2014), pp. 536-536, https://doi.org/10.1038/514536a

Abstract

Papers in Nature journals should make computer code accessible where possible. [Excerpt] A theme in Nature’s ongoing campaign for the replicability and reproducibility of our research papers is that key components of publications should be available to peers who wish to validate the techniques and results. A core element of many papers is the computercode used by authors in models, simulations and data analysis. In an ideal world, this code would always be transportable and easily used by others. In such a ...

 

Runoff simulation with eight different flow accumulation algorithms: Recommendations using a spatially distributed and open-source model

  
Environmental Modelling & Software, Vol. 62 (December 2014), pp. 11-21, https://doi.org/10.1016/j.envsoft.2014.08.025

Abstract

Flow accumulation algorithms (FAAs) predict the cumulative upstream drainage but each FAA generates a different map and this uncertainty still remains unsolved. This study makes advances in flow path research by testing 8 FAAs and analyzing the uncertainties of 15 simulations. The DR2-2013© SAGAv1.0 hydrological software is presented in a study carried out for two catchment lakes (NE Spain) over a 69-month test period. The best simulations were obtained with two single flow (Rho8 and Deterministic Infinity) and two multiple flow ...

 

GRASS GIS manual: r.horizon

  
In GRASS Development Team, 2013. GRASS GIS 6.4.3svn Reference Manual (2013)

Abstract

r.horizon - Horizon angle computation from a digital elevation model. Computes horizon angle height from a digital elevation model. The module has two different modes of operation: 1. Computes the entire horizon around a single point whose coordinates are given with the 'coord' option. The horizon height (in radians). 2. Computes one or more raster maps of the horizon height in a single direction. The input for this is the angle (in degrees), which is measured counterclockwise with east=0, north=90 etc. The ...

 

Free Software on the final frontier: GNU Radio controls the ISEE-3 Spacecraft

  
(2014)

Abstract

[Excerpt] Equipped with free GNU Radio software, a group of citizen scientists has contacted, controlled, and is attempting to recapture a 1970s-era satellite and bring it back into an orbit close to Earth. The International Sun-Earth Explorer-3, or ISEE-3, was launched in 1978 by NASA to monitor activity on the sun. After three years of observation, NASA repurposed the satellite, which soon became the first spacecraft to visit a comet. The mission ended in 1999, when NASA abandoned ISEE-3 to orbit ...

 

ObsPy: A Python Toolbox for Seismology

  
Seismological Research Letters, Vol. 81, No. 3. (01 May 2010), pp. 530-533, https://doi.org/10.1785/gssrl.81.3.530

Abstract

[excerpt] The wide variety of computer platforms, file formats, and methods to access seismological data often requires considerable effort in preprocessing such data. Although preprocessing work-flows are mostly very similar, few software standards exist to accomplish this task. The objective of ObsPy is to provide a Python toolbox that simplifies the usage of Python programming for seismologists. It is conceptually similar to SEATREE (Milner and Thorsten 2009) or the exploration seismic software project MADAGASCAR (http://www.reproducibility.org). In ObsPy the following essential seismological ...

 

Supplementary materials for: a proposal for an integrated modelling framework to characterise habitat pattern

  
(2014)

Abstract

In Estreguil et al. (Environ Modell Softw 52, 176-191, 2014), an integrated modelling framework is proposed to characterise habitat pattern. The modelling approach is there exemplified by deriving a set of twelve indices aggregated into four categories: general landscape composition, habitat morphology, edge interface and connectivity. The easy and reproducible computability is ensured with the integrated use of publicly available software (GUIDOS free-download software, Conefor free software) and of newly programmed tools. A statistical analysis is then conducted using classical linear ...

 

GRASS GIS manual: r.watershed

  
In GRASS Development Team, 2014. GRASS GIS 7.0.0svn Reference Manual (2014)

Abstract

r.watershed - Calculates hydrological parameters and RUSLE factors. ...

 

Modeling, informatics, and the quest for reproducibility

  
Journal of Chemical Information and Modeling, Vol. 53, No. 7. (12 June 2013), pp. 1529-1530, https://doi.org/10.1021/ci400197w

Abstract

There is no doubt that papers published in the Journal of Chemical Information and Modeling, and related journals, provide valuable scientific information. However, it is often difficult to reproduce the work described in molecular modeling and cheminformatics papers. In many cases the software described in the paper is not readily available, in other cases the supporting information is not provided in an accessible format. To date, the major journals in the fields of molecular modeling and cheminformatics have not established guidelines ...

 

Letter to the Editor - Comment on editorial on software distribution in science

  
Journal of Chemical Information and Modeling, Vol. 24, No. 4. (1 November 1984), pp. 276-276, https://doi.org/10.1021/ci00044a600

Abstract

I am accepting your invitation to comment on your editorial in the May issue of JCICS regarding the subject of scientists’ commercial stakes in programs that they write for scientific purposes. I feel strongly about this issue because I believe that the spirit of scientific investigation and the spirit of scientific cooperation are threatened by the behavior of some of our new entrepreneurs who desire to get rich quick. The question of vested interest can be resolved at the publication level, at ...

 

A proposal for an integrated modelling framework to characterise habitat pattern

  
Environmental Modelling & Software, Vol. 52 (February 2014), pp. 176-191, https://doi.org/10.1016/j.envsoft.2013.10.011

Abstract

[Highlights] [::] Habitat pattern characterisation as methodological guidance for fragmentation assessments (applied in Europe). [::] Reproducible integration of three landscape models with GIS and semantic array programming. [::] Four families indices: landscape composition, edge interface, habitat morphology and connectivity. [::] New indices: edge interface context of morphological shapes; Power Weighted Probability of Dispersal family for connectivity. [::] Nonlinear statistical correlation analysis based on Brownian Distance Correlation. [Abstract] Harmonized information on habitat pattern, fragmentation and connectivity is one among the reporting needs of the biodiversity policy agenda. This paper ...

 

ATLAS

  
In Free Software Directory (April 2011)
edited by Janet Casey

Abstract

ATLAS (Automatically Tuned Linear Algebra Software) is a system for generating high-performance mathematical libraries. It generates a library that is specifically tuned to your processor and compiler. ATLAS's purpose is to provide portably optimal linear algebra software. In particular, ATLAS provides ANSI C and Fortran 77 interfaces to the BLAS, and a subset of LAPACK. ...

 

mcsim

  
In Free Software Directory (April 2011)
edited by Kelly Hopkins

Abstract

'MCSim' is a simulation and statistical inference tool for algebraic or differential equation systems. While other programs have been created to the same end, many of them are not optimal for performing computer intensive and sophisticated Monte Carlo analyses. MCSim was created specifically to perform Monte Carlo analyses in an optimized, and easy to maintain environment. ...

 

Dap

  
In Free Software Directory (April 2011)
edited by Janet Casey

Abstract

Dap is a small statistics and graphics package, based on C, that provides core methods of data management, analysis, and graphics commonly used in statistical consulting practice. Anyone familiar with basic C syntax can learn Dap quickly and easily from the manual and the examples in it. Advanced features of C are not necessary, although they are available. As of Version 3.0, Dap can read SBS programs, thereby freeing the user from having to learn any C at all to run ...

 

DataStatix

  
In Free Software Directory (April 2013)
edited by Enyst

Abstract

DataStatix is a free software for GNU/Linux and Windows useful to manage data of every kind (although it has been written to manage biomedical data), to create descriptive statistics and graphs and to export items easily to R environment or to other statistic softwares. In order to handle properly big amount of data and many concurrent users, DataStatix works with MySql database and it has been developed and tested with MySql community edition 5.5. Some features of the software are: users ...

 

Mastrave

  
In Free Software Directory (October 2011), 8008

Abstract

Mastrave is a free software library written to perform vectorized scientific computing and to be as compatible as possible with both GNU Octave and Matlab computing frameworks, offering general purpose, portable and freely available features for the scientific community. Mastrave is mostly oriented to ease complex modeling tasks such as those typically needed within environmental models, even when involving irregular and heterogeneous data series. [Semantic array programming]. The Mastrave project attempts to allow a more effective, quick interoperability between GNU Octave and Matlab ...

 

MedianTracker

  
In Free Software Directory (April 2011)

Abstract

MedianTracker supports efficient median queries on and dynamic additions to a list of values. It provides both the lower and upper median of all values seen so far. Any __cmp__()-able object can be tracked, in addition to numeric types. add() takes log(n) time for a tracker with n items; lower_median() and upper_median() run in constant time. Since all values must be stored, memory usage is proportional to the number of values added (O(n)). ...

 

OptionMatrix

  
In Free Software Directory (April 2013)

Abstract

These calculators are real-time multi-model option chain pricers with analytics and interactive controls. optionmatrix is the GTK+ graphical user interface version and optionmatrix_console is the Curses version. Both programs feature: greeks, decimal date to real-date translations, real-date to decimal date translations, real-time time bleeding, configurable option expiration date engines, calendars, strike control systems, tickers and over 135 option models. optionmatrix also supports: spreads, bonds, term structures, cash flow editing, source code viewing and text exporting. ...

 

Bc

  
In Free Software Directory (April 2011)

Abstract

'Bc' is an arbitrary precision numeric processing language. Its syntax is similar to C, but differs in many substantial areas. It supports interactive execution of statements. 'Bc' is a utility included in the POSIX P1003.2/D11 draft standard. This version does not use the historical method of having bc be a compiler for the dc calculator (the POSIX document doesn't specify how bc must be implemented). This version has a single executable that both compiles the language and runs the resulting 'byte ...

 

Autoclass

  
In Free Software Directory (April 2011)

Abstract

AutoClass solves the problem of automatic discovery of classes in data (sometimes called clustering or unsupervised learning), as distinct from the generation of class descriptions from labeled examples (called supervised learning). It aims to discover the 'natural' classes in the data. AutoClass is applicable to observations of things that can be described by a set of attributes, without referring to other things. The data values corresponding to each attribute are limited to be either numbers or the elements of a fixed ...

 

Apophenia

  
In Free Software Directory (April 2011)

Abstract

'Apophenia' is a statistical library for C. It provides functions on the same level as those of the typical stats package (OLS, probit, singular value decomposition, &c.) but doesn't tie the user to an ad hoc language or environment. It uses the GNU Scientific Library for number crunching and SQLite for data management, so the library itself focuses on model estimation and quickly processing data. ...

 

PSPP

  
In Free Software Directory (April 2011)

Abstract

PSPP is a program for statistical analysis of sampled data. It is a Free replacement for the proprietary program SPSS. ...

 

Toward reproducible computational research: an empirical analysis of data and code policy adoption by journals

  
PLOS ONE, Vol. 8, No. 6. (21 June 2013), pp. e67111-e67111, https://doi.org/10.1371/journal.pone.0067111

Abstract

Journal policy on research data and code availability is an important part of the ongoing shift toward publishing reproducible computational science. This article extends the literature by studying journal data sharing policies by year (for both 2011 and 2012) for a referent set of 170 journals. We make a further contribution by evaluating code sharing policies, supplemental materials policies, and open access status for these 170 journals for each of 2011 and 2012. We build a predictive model of open data ...

 

Better living through transparency: improving the reproducibility of fMRI results through comprehensive methods reporting

  
In Cognitive, Affective, & Behavioral Neuroscience (2013), pp. 1-7, https://doi.org/10.3758/s13415-013-0188-0

Abstract

Recent studies suggest that a greater proportion of published scientific findings than expected cannot be replicated. The field of functional neuroimaging research is no exception to this trend, with estimates of false positive results ranging from 10 % to 40 %. While false positive results in neuroimaging studies stem from a variety of causes, incomplete methodological reporting is perhaps the most obvious: Most published reports of neuroimaging studies provide ambiguous or incomplete descriptions of their methods and results. If neuroimaging researchers do not ...

 

GRASS GIS manual: r.sun

  
In GRASS Development Team, 2013. GRASS GIS 6.4.3svn Reference Manual (2007)

Abstract

r.sun - Solar irradiance and irradiation model. Computes direct (beam), diffuse and reflected solar irradiation raster maps for given day, latitude, surface and atmospheric conditions. ...

 

How to scale a code in the human dimension

  
(29 Jan 2013)

Abstract

As scientists' needs for computational techniques and tools grow, they cease to be supportable by software developed in isolation. In many cases, these needs are being met by communities of practice, where software is developed by domain scientists to reach pragmatic goals and satisfy distinct and enumerable scientific goals. We present techniques that have been successful in growing and engaging communities of practice, specifically in the yt and Enzo communities. ...

This page of the database may be cited as:
Integrated Natural Resources Modelling and Management - Meta-information Database. http://mfkp.org/INRMM/tag/free-scientific-software

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Meta-information Database (INRMM-MiD).
This database integrates a dedicated meta-information database in CiteULike (the CiteULike INRMM Group) with the meta-information available in Google Scholar, CrossRef and DataCite. The Altmetric database with Article-Level Metrics is also harvested. Part of the provided semantic content (machine-readable) is made even human-readable thanks to the DCMI Dublin Core viewer. Digital preservation of the meta-information indexed within the INRMM-MiD publication records is implemented thanks to the Internet Archive.
The library of INRMM related pubblications may be quickly accessed with the following links.
Search within the whole INRMM meta-information database:
Search only within the INRMM-MiD publication records:
Full-text and abstracts of the publications indexed by the INRMM meta-information database are copyrighted by the respective publishers/authors. They are subject to all applicable copyright protection. The conditions of use of each indexed publication is defined by its copyright owner. Please, be aware that the indexed meta-information entirely relies on voluntary work and constitutes a quite incomplete and not homogeneous work-in-progress.
INRMM-MiD was experimentally established by the Maieutike Research Initiative in 2008 and then improved with the help of several volunteers (with a major technical upgrade in 2011). This new integrated interface is operational since 2014.